Phylogenetic relationships between Nostoc cyanobionts in the lichen genus Pannaria were studied to evaluate their correlation to geography, habitat ecology, and other patterns previously reported. The 16S rRNA gene sequences of a total of 37 samples of 21 Pannaria species from seven countries from the Northern and Southern hemispheres were analyzed and compared with 69 free-living and symbiotic cyanobacterial strains. The sequences from Pannaria were distributed throughout a branch of Nostoc sequences previously called “the Nephroma guild,” and within two subgroups from another branch, referred to as the “Peltigera guild,” although there was a gradual transition between the two major groups. There is a more diverse pattern of relationships between Nostoc sequences from bipartite versus tripartite lichen species in Pannaria, compared with other well-studied genera, such as Nephroma and Peltigera. Cyanobionts from several tripartite Pannaria species from the Southern Hemisphere and corticolous bipartite species from both hemispheres were grouped together. Four sequences of Pannaria and Pseudocyphellaria cyanobionts from rocks in the Chilean Juan Fernández Islands were nested within corticolous cyanobionts, whereas the terricolous “Pannaria sphinctrina clade” was placed with other terricolous strains. The cluster patterns derived from phylogenetic analysis were partly reflecting lichen taxonomy, in two groups of lichen species, possibly indicating coevolution. The phylogram partly also reflected lichen ecology. Three Pannaria species have very different cyanobiont strains when they grow in different habitats.